Showing : network • reset
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 3.4 years ago by ▴ 730 • written 7.6 years ago by ▴ 40
8
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4
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6.9k
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WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by ▴ 180
7
votes
1
reply
3.4k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq network limma
updated 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 250
7
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9
replies
3.6k
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WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 15 months ago by ★ 3.0k • written 5.0 years ago by ▴ 10
5
votes
2
replies
4.1k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 4.2 years ago by ★ 3.9k • written 4.2 years ago by ▴ 30
5
votes
14
replies
4.8k
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Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 8.4 years ago by ★ 8.2k • written 8.4 years ago by ▴ 50
4
votes
3
replies
901
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WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 5.0 years ago by ★ 3.0k • written 5.0 years ago by ▴ 80
4
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2
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1.1k
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iSEE - Custom Panel
Network GeneNetwork iSEE
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
3
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2
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5.0k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 23 months ago by ▴ 10 • written 3.7 years ago by ▴ 80
2
votes
6
replies
4.6k
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Error running TOMplot in WGCNA package
wgcna network
updated 9.6 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
2
votes
4
replies
1.8k
views
Case-control study using WGCNA
wgcna network rna-seq
4.4 years ago ag1805x ▴ 80
2
votes
1
reply
1.4k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
2
votes
1
reply
783
views
WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 19 months ago by ▴ 50 • written 19 months ago by ▴ 10
2
votes
0
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506
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Quality Metrics for Graph Clustering for Biological Networks
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3.9 years ago hamza_karakurt ▴ 50
2
votes
5
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1.3k
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runing NetBenchmark on my own datasets
software error network
updated 8.5 years ago by ▴ 20 • written 8.5 years ago by ▴ 40
1
vote
1
reply
1.5k
views
Custom scoring for subnetworks in BioNet
bionet network
updated 7.9 years ago by ▴ 120 • written 7.9 years ago by ▴ 660
1
vote
1
reply
824
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 3 months ago by ▴ 20 • written 4 months ago by ▴ 90
1
vote
1
reply
1.5k
views
WGCNA gene clusters vs eigengenes
wgcna network coexpression eigengenes
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 10
1
vote
1
reply
1.3k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna coexpression cooccurrence coabundance network
updated 6.5 years ago by ▴ 730 • written 6.6 years ago by ▴ 40
1
vote
2
replies
1.3k
views
Additional high-scoring subnetworks in BioNet
bionet network
updated 7.9 years ago by ▴ 120 • written 7.9 years ago by ▴ 660
1
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10
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2.0k
views
Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 17 months ago by • 0
1
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2
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4.0k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 9.6 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
1
vote
7
replies
2.7k
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Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
9.5 years ago pshannon ▴ 100
1
vote
1
reply
1.4k
views
WGCNA_ Eigengene and sample complications correlations
Network Network
updated 9.8 years ago by ★ 3.0k • written 9.8 years ago by ▴ 130
1
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2
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2.8k
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cnetplot() - library(clusterProfiler)
clusterProfiler network
8.9 years ago cristina della beffa ▴ 30
0
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0
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1.1k
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JOB: Biostatistican
Microarray Genetics Proteomics Network Kidney Microarray Genetics Proteomics Network
20.6 years ago Robert Campanell ▴ 10
0
votes
0
replies
1.1k
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[SPAM?] Bioconductor Digest, Vol 41, Issue 22 (Out of Office)
SNP Microarray Annotation GO Network Clustering Survival Cancer hgu133a cdf probe affy
17.8 years ago Todd Nick ▴ 10
0
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0
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847
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B value cutoff in LIMMA
Network Cancer limma Network Cancer limma
18.1 years ago Gordon Smyth 50k
0
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0
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663
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Problem downloading Bioconductor
Network Network
17.9 years ago Seth Falcon ★ 7.4k
0
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0
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643
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Greek characters and subscripts in network graphs
Network Rgraphviz Network Rgraphviz
17.4 years ago Martin Henry H. Stevens ▴ 10
0
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0
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1.1k
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Biocore response to Affymetrix data format changes
Microarray GO Network Cancer cdf affy PROMISE Microarray GO Network Cancer cdf affy
20.8 years ago Kulp, David ▴ 20
0
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0
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1.1k
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Fwd: ASSIST on contrast matrix
Network Homo sapiens limma PROcess Network Homo sapiens limma PROcess
11.7 years ago Seyed Ahmad Mousavi ▴ 10
0
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0
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747
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no connection to biol
Network Network
18.2 years ago Francois Pepin ★ 1.3k
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3
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1.9k
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Drawing network graphs (i.e. nodes and edges)
Network Network
updated 18.2 years ago by ▴ 360 • written 18.2 years ago by ▴ 170
0
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0
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Affymetrix Software Development Conference Early Registration rat es - final days
SNP GO Network BEAT SNP GO Network BEAT
21.0 years ago DevNet ▴ 20
0
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0
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need a neural network package for microarray data analysis
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18.4 years ago Stephen Henderson ★ 1.0k
0
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0
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821
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Bug in maNormNN
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18.5 years ago Tarca, Adi ▴ 570
0
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1
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906
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Re: Try to run a lots of chips: 32 bits vs 64 bits
Normalization GO Network Normalization GO Network
updated 21.2 years ago by ▴ 530 • written 21.2 years ago by ▴ 430
0
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0
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743
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BioPAX/SBPAX import for MicroArray Analysis and Hypothesis Building
Microarray Network Microarray Network
11.9 years ago Oliver Ruebenacker ▴ 110
0
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0
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BioC 1.9 is released!
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17.6 years ago Seth Falcon ★ 7.4k
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help with bayesian network
Network Bayesian Network Bayesian
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0
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KEGG analysis
Network Cancer Network Cancer
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vacancy postdoc or PhD in the Netherlands
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15.1 years ago Hendriks, M. ▴ 10
0
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2
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Affymetrix MASv5 code & sample data
Network Network
updated 18.9 years ago by ★ 1.8k • written 18.9 years ago by ▴ 50
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3
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building enzyme centric metabolic network
Network KEGGSOAP Network KEGGSOAP
updated 15.0 years ago by 25k • written 15.0 years ago by ▴ 270
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Post Doc position, Berlin Germany
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Software Demo for Summer Research Grant
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bioinformatics programmer position
Network Network
14.8 years ago Wall, Dennis Paul ▴ 80
0
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Invitation to connect on LinkedIn
Network Network
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Pathview question
Network convert pathview Network convert pathview
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50 results • Page 1 of 1
Recent ...
Replies
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Answer: get BM error by James W. MacDonald 65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Answer: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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